Graph Cleaning

  usage: mccortex31 clean [options] <in.ctx> [in2.ctx ...]

    Clean a cortex graph. Joins graphs first, if multiple inputs given.
    If neither -T or -U specified, just saves output statistics.

    -h, --help                  This help message
    -q, --quiet                 Silence status output normally printed to STDERR
    -f, --force                 Overwrite output files
    -o, --out <out.ctx>         Save output graph file [required]
    -m, --memory <mem>          Memory to use
    -n, --nkmers <kmers>        Number of hash table entries (e.g. 1G ~ 1 billion)
    -t, --threads <T>           Number of threads to use [default: 2]
    -N, --ncols <N>             Number of graph colours to use

    Cleaning:
    -T, --tips <L>              Clip tips shorter than <L> kmers
    -U[X], --unitigs[=X]        Remove low coverage unitigs with coverage < X [default: auto]
    -B, --fallback <T>          Fall back threshold if we can't pick

    Statistics:
    -c, --covg-before <out.csv> Save kmer coverage histogram before cleaning
    -C, --covg-after <out.csv>  Save kmer coverage histogram after cleaning
    -l, --len-before <out.csv>  Save unitig length histogram before cleaning
    -L, --len-after <out.csv>   Save unitig length histogram after cleaning

    --unitigs without a threshold, causes a calculated threshold to be used
    Default: --tips 2*kmer_size --unitigs

Plot a unitig coverage histogram using R + ggplot2:

 R --vanilla --file=<CORTEX_PATH>/scripts/plot-covg-hist.R --args covg.csv covg.pdf

Plot a unitig length histogram:

R --vanilla --file=<CORTEX_PATH>/scripts/plot-length-hist.R --args len.after.csv len.after.pdf